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Analysis of intermediate filament structure by chemical cross-linking
Dlabolová, Lada ; Novák, Petr (advisor) ; Šulc, Miroslav (referee)
Intermediate filament proteins create a dynamic cytoskeletal filamentous network, which due to its elastic properties, significantly contributes to the resistance of cells and tissues to mechanical stress. An important protein from the family of intermediate filaments, vimentin, is expressed mainly in cells of mesenchymal origin. Vimentin has been associated with a large number of pathophysiological conditions, and current studies consider vimentin as clinically promising target for the diagnosis, prognosis and treatment of a wide range of diseases from cancer to infectious and inflammatory diseases. Although in terms of structural characterization, vimentin belongs to one of the most studied proteins from the family of intermediate filaments, our knowledge is currently limited to the structure of the vimentin tetramer. Vimentin is capable of self-assembly into filaments formed by homo-oligomeric ULF subunits and the assembly process involves several steps of the organization of subunits. Structural characterization of the oligomeric subunits involved in the assembly of vimentin filaments is a prerequisite for elucidating the architecture of mature filaments, which can significantly contribute to understanding and connecting the mechanisms of many diseases associated with changes in vimentin...
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Structure and interaction of human 14-3-3 regulatory protein using in vitro photoaffinity labelling in combination of protein nano-probes and mass spectrometry
Mazurová, Martina ; Šulc, Miroslav (advisor) ; Dračínská, Helena (referee)
This thesis is focused on the study of the structure and mechanism of human 14- 3-3 protein, which is one of the important regulatory proteins present in all eukaryotic cells. Nowadays it is known seven isoforms of this protein in mammals. Although their crystal structure shows a high similarity, their mutual comparison reveals some changes. The aim of this work is to prepare experimental tools for verification whether the differences in the crystal structure of the ζ isoform are present in solution and how the structure-functional mechanism of this isoform is affected. The otimization of 14-3- 3zeta recombinant protein expression with incorporated a photo-labile analog of leucine in the protein sequence was performed using limiting medium with prokaryotic expression system of E. coli BL-21 DE3 Gold or system of auxotrophic E. coli K-12 with non-functional leucine biosynthesis.
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Functional analysis of insect fatty acyl-coenzyme A reductases and desaturases
Tupec, Michal ; Pichová, Iva (advisor) ; Šulc, Miroslav (referee) ; Doležel, David (referee)
Fatty acid-derived lipids are an important class of biomolecules. In addition to their primary role in cellular architecture, energy storage and signaling, they function in many other ways, e.g. as isolating or waterproof coatings, defense compounds and pheromones. Multiple enzymes mod- ify intermediates originating from fatty acid biosynthetic pathway, including desaturases (FADs) which synthesize unsaturated fatty acids, and reductases (FARs) which synthesize fatty alcohols. Functionally highly diversified fatty acyl-modifying enzymes from insects, one of the most abun- dant animals in the world, present a significant source for modern biotechnology of cell factories. This thesis summarizes available information on the FADs and FARs and describes the results which we have obtained while studying them. In bumblebees, we identified several FAR transcripts which are abundantly expressed in male pheromone-producing tissue. We then functionally characterized the corresponding enzymes in yeasts, and estimated their participation in the biosynthesis of fatty alcohols observed in the mark- ing pheromone-producing tissue. The studied enzymes reduce broad range of substrates, from short fatty acyls (e.g. C14) to very long ones (e.g. C26), from saturated fatty acyls to polyunsatu- rated ones. We also found...
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Structure-function relationship of Kingella kingae RtxA toxin.
Růžičková, Eliška ; Osička, Radim (advisor) ; Šulc, Miroslav (referee)
Kingella kingae is a pediatrically significant, facultative pathogen. It asymptomatically colonizes the oropharynx of young children, where it is a part of the normal microflora. However, if it penetrates the respiratory epithelial barrier and begins to spread throughout the body, it can cause serious infectious diseases. Thanks to today's advanced diagnostic methods, K. kingae is included among important human pathogens, and in pediatric patients, K. kingae is reported as a frequent cause of osteoarticular infections, such as osteomyelitis and septic arthritis, bacteremia, and endocarditis. The key virulence factor of this bacterium, the cytotoxin RtxA, belongs to the RTX (Repeats in ToXin) toxin family. This family of toxins shares several characteristic features: (i) the presence of a hydrophobic pore-forming domain in the N-terminal part of the molecule containing several predicted transmembrane α-helices (ii) the inactive protoxin is activated by different types of fatty acids bound to specific lysine residues in the acylated domain, (iii) the presence of nonapeptide repeat sequences, rich in glycine and aspartate residues, that are important for the binding of calcium ions, (iv) the presence of a C-terminal secretion signal that is recognized by the type I secretion system (T1SS), and (v)...
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Structure and function of RTX toxins of Gram-negative bacteria
Zhuk, Karyna ; Osička, Radim (advisor) ; Šulc, Miroslav (referee)
RTX toxins (Repeats in ToXin) are produced by Gram-negative bacteria, most of which are important human or animal pathogens. The polypeptide chain of each RTX toxin consists of four conserved regions. An N-terminal hydrophobic domain, which is important for insertion of the RTX toxin into the host cell membrane and pore formation. The hydrophobic domain is followed by an acylated segment containing conserved lysine residues, at which the toxin is acylated and thus activated. The C-terminal portion of each RTX toxin contains a repeat domain to which calcium ions bind. The C-terminus of the toxin contains a secretion signal that is recognized by the type I secretion system, which transports the toxin from the bacterial cytosol to the external environment. After secretion, RTX toxins interact with the cell surface via specific β2 integrins and/or glycosylated structures such as glycoproteins and gangliosides or membrane components such as sphingomyelins and cholesterol. Once bound to the cell, RTX toxin monomers insert into the membrane and oligomerize to form pores. The uncontrolled flow of ions through these pores can lead to disruption of bactericidal functions of myeloid phagocytes, stimulation or suppression of the release of pro-inflammatory cytokines, modulation of various signaling and...
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Proteomická a bioinformatická charakterizace N-terminálních sekvencí proteinů modifikovaných po importu do hydrogenosomu Trichomonas vaginalis.
Zákoucká, Eva ; Man, Petr (advisor) ; Šulc, Miroslav (referee)
Trichomonas vaginalis is a human pathogen causing trichomoniasis, one of the most common non-viral sexually transmitted diseases in both men and women. Trichomoniasis is currently treated with metronidazole, but the pathogen is known to develop resistance against this drug. However as the pathogen is eukaryotic, the targets for the pathogen elimination without seriously affecting the host are limited. Throughout the evolution Trichomonas vaginalis adapted to anaerobic environments by developing an alternative metabolism resulting in a reduced form of mitochondria named hydrogenosome. Hydrogenosomes lack genetic information, therefore all its proteins are nucleus-encoded and need to be transported inside the hydrogenosome using a targeting N-terminal presequence. The peptidase recognizing and cleaving those presequences at the entrance of the organelle, the hydrogenosomal processing peptidase (HPP), is unique for hydrogenosomes and therefore represents a potential drug target against the pathogen. In this work the HPP's substrate specificity towards the targeting presequences was investigated. To do so a proteomic analysis of the proteome of Trichomonas vaginalis hydrogenosomes was performed using a novel optimized protocol for N-terminal peptide sequencing. N-terminal peptides were captured using a...
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Analogues of IGF-1 for the study of interactions of the hormone with the receptors for IGF-1 and insulin
Macháčková, Kateřina ; Jiráček, Jiří (advisor) ; Obšilová, Veronika (referee) ; Šulc, Miroslav (referee)
Insulin/IGF system is a complex network of three similar hormones (insulin, IGF-1 and IGF-2) and their three similar receptors (IR-A, IR-B and IGF-1R,), which play important roles in maintaining basal energy homeostasis of the organism, in growth, development, life-span but also in development of diseases such as diabetes mellitus, cancer, acromegaly or Laron dwarfism. Despite structural similarities between family members, each member have its unique role in the system. Identification of structural determinants in insulin and IGFs that trigger their specific signalling pathways is important for rational drug design for safer treatment of diabetes or for more efficient combating of cancer or growth-related disorders. In this thesis, we focused on identification of such structural determinants in IGF-1. Comparison of our data with parallel studies with IGF-2 and insulin could give a more complex picture of the problem. First of all, we developed necessary methodologies for the preparation of IGF-1 analogues. We developed a new methodology for the total chemical synthesis of IGF-1 analogues based on the solid-phase synthesis of fragments and their ligation by a CuI -catalyzed cycloaddition of azides and alkynes. In parallel, we developed a procedure for a recombinant production of IGF- 1 and its...
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